Dr. Wile’s Tirade Against Evolution Continues…

Earlier this month, I wrote a criticism of a couple of videos produced by the Creation Museum that attacked a video made by the engineer and science educator Bill Nye. A commenter alerted me to a response by a Dr. Wile in the comment section on his blog. Dr. Wile is a young-earth creationist with a PhD in nuclear chemistry from the University of Rochester, who has experience with education (having written a couple of homeschooling textbooks on science as well as taught courses in science). In response, I wrote another response rebutting the claims made by Dr Wile.

Now, Dr. Wile has graciously taken the time to write a reply to my second post. It demonstrates the typical rhetoric and debating methods of creationists together with well-known evasion tactics. Let’s examine it in detail.

Evolution denial, uniqueness and the U. S.

Of course, Nye is saying nothing of the sort. Nowhere in Nye’s statement can you find the words “large proportion.” In addition, while Nye certainly mentions technological advancement, he is using it as a descriptor for the United States, not a qualifier for his statement. Regardless of the mental gymnastics of Mr. Karlsson, Nye’s statement is unambiguously false.

When communicating with other people, or interpreting the words of other people, there are at least two common paradigms. Both involves listening to the other person, but with very different intentions and goals. The first is about listening in order to gather ammunition for a retort. This is characterized by interpreting the other person as literally as possible and getting hung up on certain phrases or words as if they negated context. Here is a hypothetical example:

Interrogator: Did you smash the windshield of Mr. X’s car?

Innocent suspect: No. I mean, I don’t like the guy and he annoys me to no end, but I would never go so far as to destroy his property just because we did not get along. Besides, I was having lunch at the cafeteria when it happened.

Interrogator: So you are saying that you don’t like the guy, that he annoys you and that you did not get along? That’s interesting. You wanted to do something about it right? Like smash his windshield of his car to make him pay for what he did to you?

It is easy to understand that the interrogator is listening to what the suspect is saying because he wants to gather ammunition for a retort, hoping to make the suspect confess, rather than being interested in what actually happened.

Another common paradigm is listening actively to others, trying to understand what they mean, rather than getting stuck on certain phrasings. It also means trying to interpret what the other person say in a charitable manner. Let’s return to our hypothetical situation:

Interrogator: Did you smash the windshield of Mr. X’s car?

Innocent suspect: No. I mean, I don’t like the guy and he annoys me to no end, but I would never go so far as to destroy his property just because we did not get along. Besides, I was having lunch at the cafeteria when it happened.

Interrogator: So you are saying that while you didn’t like the guy, you are not the type of person who would take it out on his car and that you were really at a different place at the time, giving you an alibi?

The difference is huge, isn’t it?

I think it is clear that Dr. Wile is applying the former perspective, rather than the latter. This is evident when Dr. Wile responds by saying that you cannot find the words “large proportion” in what Bill Nye said. While this is true, it is irrelevant because we are dealing with interpretation, not merely literal readings of transcripts. Many young-earth creationists are biblical literalists, so it may be difficult to switch mode at times. This does not excuse Dr. Wile’s approach, but may give us additional background for why Dr. Wile has decided to select such an approach in this conversation.

If we understand the immediate context of the video (i.e. Bill Nye is pointing out that the U. S is perhaps the most technologically advanced nations in the world, yet has a huge proportion of individuals who deny evolution) and the larger context of e. g. the research (showing that the U. S. has by far the highest proportion of creationists among industrialized, western nations), we can understand why he considers the U. S. unique.

However, let’s assume Mr. Nye really did mean what Mr. Karlsson claims, even though Mr. Nye said something completely different. Even if that’s the case, his statement is still a complete fabrication. Would Mr. Karlsson agree that Germany is technologically advanced? The study to which he refers indicates that more than 20% of its population denies evolution. The same is true of Italy, Spain, the Netherlands, and Switzerland. In the U.S., a larger percentage (roughly 40%) deny evolution, but that’s not drastically different from the percentage found in many other technologically-advanced nations. Even in the U.K., the percentage of people who deny evolution is greater than 15%.

Of course, the uniqueness that Bill Nye is talking about is a quantitative uniqueness, not a qualitative one. Obviously, he probably does not believe that creationism is non-existent in other technologically advanced nations. Other western, industrialized nations do have a small to moderate proportion of creationists, but even if we take Germany, the U. S. has twice the proportion of creationists than Germany (around a 20 percentage point difference). As far as I can see, this makes the U. S. unique in a certain sense.

So the end of the line is that Bill Nye is claiming that the U. S. is one of the most technologically advanced nations in the world, yet have an exceptionally high proportion of creationists that is much larger than any other country in this group. He this that this, in some sense, makes the U. S. unique. This is a very reasonable interpretation of what is being said and it is factually true.

2. False Balance

Mr. Karlsson originally claimed that in order to teach creationism, you have to teach scientific falsehoods. I pointed out that this is completely false. He couldn’t defend his false statement. Instead, after admitting that he has not analyzed my books, he claims that they “must” be teaching scientific falsehoods if they teach creationism. Obviously, such evidence-free statements have no merit.

My general argument was that if one teach creationism together with evolution and pretend that they are of either of equal merit, or that creationism has more scientific merit than evolution, one is appealing to false balance. This is an extremely common creationist tactic, especially in a legal context (e. g. equal-time laws). The reason this is a bad idea is because they do not have equal scientific merits. Evolution is supported by a vast mountain of scientific evidence and there is no scientific debate regarding if common descent is true. There may be vitriolic debates regarding the relative merits of different mechanisms or which branch is closest to which, but that is something completely different.

Evolution is based on a massive amount of scientific evidence. Reading any introductory textbook or paper on the subject shows this, such as 29+ Evidences for Macroevolution: The Scientific Case for Common Descent.

He then takes issue with my statement that my books produce excellent university-level science students. He says that I produce “just three anecdotes” to support the position. While it’s true that I chose to list only three examples in that article, there are many more.

I pointed out that Dr. Wile has not really provided any evidence that his books produce excellent university-level science students. He provided a couple of anecdotes. So what does Dr. Wile have to say in response to my criticisms? He provides additional anecdotes. Hardly convincing.

He then makes some statements that imply I claimed my books produce such excellent university students because they contain creationism. I said no such thing. I simply pointed out that students who use my books do very well at university, which is rather hard to imagine if they were filled with the scientific falsehoods that Mr. Karlsson claims “must” be in them.

Dr. Wile also did not reply to any of the criticisms I made of his argument given that we assume that his books does, in fact, produce excellent university-level science students. Instead, he made a straw man argument.

What Dr. Wile argued was, as I have understood it, that his textbooks contain creationism, yet produce excellent university students and that this meant that it was unlikely that his books contain scientific falsehoods about evolution. My counterargument was that this was an unpersuasive argument, because the assumed fact that his books produce excellent university students in science is entirely consistent with containing scientific falsehoods if any number of things are true, such as:

(1) Dr. Wile could be extremely good at writing textbooks and explaining scientific concepts (besides evolution obviously), so the effects of the scientific falsehoods on evolution is dwarfed by the excellence of the other material he discusses

or

(2) perhaps homeschooling is just so much more effective than public education in terms of e. g. exam performance (due to, maybe, higher teacher:student ratios?) that this outweighs the effects of teaching scientific falsehoods on evolution.

Obviously, I do not know that any of these two points are true, but they are some of the confounders that needs to be eliminated in order for Dr. Wile’s argument to be rationally persuasive. Dr. Wile has not attempted to do so. This means that my objection stands unharmed.

3. Gene duplication

In my previous post, I provided a number of evidence-based examples of how gene duplication and subsequent divergence produce increased genetic information (for any reasonable definition of the term). What does Dr. Wile do in response? He says that the first reference is from a textbook, and the other (from Nature) just contain postulated mechanisms, but no evidence. He then goes on to ignore the other 10 or so examples I provided.

For example, his second reference is an article in Nature, which simply explains how the adaptive immune system in mammals is “believed” to have started by two rounds of whole genome duplication. Once again, such postulations can be made, but they are not in line with direct observation.

Since Dr. Wile is either unable or unwilling to engage the specific details of the science on the rest of the examples, one can only conclude that he is forced to concede the point. However, I will go into more detail with regards to this second reference (a detailed discussion of all 12 examples I provided would take up far too much space and time), because Dr. Wile’s misunderstandings of the science of the paper is particularly embarrassing.

First of all, the paper is not about the origin of adaptive immunity in mammals. The ancestors of mammals already had an adaptive immune system. Rather, it is about the origin of the vertebrate adaptive immune system as well as the adaptive immune system in organisms such as hag fish and lamprey (which differs from that of vertebrates). This leads me to conclude that Dr. Wile have not read the paper in question before writing his response. In fact, because he thinks it is about the adaptive immune system in mammals, he has probably just read part of the first sentence of the abstract.

Abstract: The adaptive immune system (AIS) in mammals, which is centred on lymphocytes bearing antigen receptors that are generated by somatic recombination, arose approximately 500 million years ago in jawed fish. This intricate defence system consists of many molecules, mechanisms and tissues that are not present in jawless vertebrates. Two macroevolutionary events are believed to have contributed to the genesis of the AIS: the emergence of the recombination-activating gene (RAG) transposon, and two rounds of whole-genome duplication. It has recently been discovered that a non-RAG-based AIS with similarities to the jawed vertebrate AIS – including two lymphoid cell lineages – arose in jawless fish by convergent evolution. We offer insights into the latest advances in this field and speculate on the selective pressures that led to the emergence and maintenance of the AIS.

The full-text version of the article can be found here.

Alright, so Dr. Wile claims that this article “simply explains how the adaptive immune system in mammals is “believed” to have started by two rounds of whole genome duplication” and that “such postulations can be made, but they are not in line with direct observation”. Is this really what the paper does? Unsurprisingly, no.

The paper discusses two important things related to the origin of the vertebrate immune system: the two whole genome duplications and the invasion of the RAG transposon. It also provides scientific evidence for these two events.

RAG is an enzyme in vertebrates that mediate recombination between different regions in the genome of e. g. a B cell. This process is called V(D)J-recombination and is responsible for a large proportion of the diversity in adaptive immunity. This diversity allows the body to respond to a large number of different foreign peptides coming from pathogens that invade our bodies. How did this mechanism arise? Evidence started appearing in the 1970s suggesting that it was due to an invasion of a transposon from a pathogen. Today, the evidence is overwhelming and includes:

• RAG sequence resembles known bacterial transposons.
• RAG 1 and RAG 2 are physically very close in the genome, consistent with being part of the original transposon.
• Between the V D and J region sits sequences called recombination signal sequences (RSSs) that are recognized by RAG, allowing recombination to occur. These RSSs closely resembles to those associated with bacterial transposons.
• RAG proteins can insert stretches of DNA into another in vitro. In vertebrates, RAG is only used for cleaving out the V, D and J regions, but bacterial transposons can do both.

Together, these provide a powerful case for the RAG invasion model. The last piece of evidence is especially persuasive: if RAG is not a bacterial transposon that invaded the genome why should it be able to act like one despite the fact that it does not do any insertions in the human body?

Now, if Dr. Wile decides to respond, I think he will try to rationalize each piece of evidence separately. But that will not work, because he needs to explain why the evidence independently converge on the same general conclusion of RAG invasion if it did not occur. It is not enough to spread uncertainty and doubt. Dr. Wile will need to explain away each piece of evidence, explain why the evidence converges on a wrong conclusion and provide an explanation that can explain the evidence better than RAG transposon invasion. Appealing to a creator or intelligent designer will not due, because the specific intentions with regards to design choices cannot be tested.

What about the two whole genome duplications (2R model)? What evidence is there for that? Evidence for that includes the fact that paralogs that emerged close to the origin of vertebrate do not have a random distribution, but occurs in clusters of four on multiple chromosomes. Perhaps the strongest piece of evidence for the 2R model is the existence of widespread quadruple conserved synteny. The Flajnik and Kasahara (2010) paper writes that:

Recently, comparison of the human and amphioxus (Branchiostoma floridae) genomes revealed widespread quadruple conserved synteny, in which four sets of human paralogons corresponded to one set of linked genes in B. floridae131. This observation provided definitive evidence for the 2R hypothesis and settled the long-standing debate.

So either Dr. Wile has to accept the 2R model or he needs to explain why the designer decided to create widespread quadruple conserved synteny to make it appear as if vertebrates have gone through two whole genome duplications. Presumably, Dr. Wile does not believe that the designer is a deceptive one, so it seems implausible that Dr. Wile will pick that horn of the dilemma.

As mentioned previously, Dr Wile has failed to comment on any of the ten remaining examples of gene duplications with subsequent divergence that leads to an increase in genetic information and has not bothered to engage with the research on two examples he did decide to comment on. Embarrassing and unfortunate.

The paper demonstrates that as a duplicated gene mutates from its originally-functional form, it gets down-regulated. That means it rarely gets “sampled” by the organism. Thus, even if mutations eventually produced the wildly improbable result of an innovative protein, the organism would not be able to benefit from it, since it is no longer used.

Actually, the paper shows that this particular gene duplication did not result in adaptive evolution. But that says nothing about gene duplication generally. Furthermore, regulation of gene expression is something that occurs on the level of an individual, usually in time-periods of minutes to hours. The fact that this particular experiment showed down-regulation has no impact on the evolutionary situation, which of course are on the time span of many generations.

Mr. Karlsson also mischaracterizes the CMI article I linked on this subject. For example, he claims that the article says gene duplication can benefit plants. It certainly says that, but it then goes on to say, “although few researchers argue that it plays a significant role in large scale evolution.” Also, when discussing benefits to the plant, it is talking only about gene duplication, not gene duplication followed by mutation, which is what Mr. Karlsson falsely claim can lead to evolutionary innovation.

Both retorts are irrelevant. The CMI article admits that gene duplication is common in plants and is beneficial. This refutes the common creationist claim that gene duplication is unable to produce anything beneficial. The only reason I brought it up is because of the irony inherent in linking to such an article in order to attack gene duplication, since it actually admits what it admits. Of course all forms of gene duplication will be followed by mutation. There is no part of the plant genome that is permanently immune to mutations. The segments that show a strong degree of conservation among plants only show an evolutionary immunity to mutations (because those that had mutations that disabled important gene products either died or where incrementally selected against).

The C-value straw man

The article correctly points out that if gene duplication followed by mutation drives evolutionary innovation, then a highly-evolved organism must have a large genome size, since many duplication events would have been necessary for the innovation to occur. We know that genome size does not correlate with an organism’s complexity, which tells us that there is something wrong with the idea that gene duplication followed by mutation can produce evolutionary innovation.

This statement explains a fundamental misunderstanding that Dr Wile has about evolution. The C-value paradox is the discovery that genome size does not correlate with complexity (in the common sense version of the word) of organism. For example, humans, considered by many to be more “complex” than, say, Arabidopsis does not have a larger genome. This is an important discovery, but does not have the implications that Dr. Wile thinks.

Why? Because Dr. Wile seem to consider evolution to be like a ladder. The most “highly-evolved” organisms at the top, with the least “highly-evolved” organisms at the bottom. Then it would make sense to appeal to the C-value paradox. More highly evolved organisms would have gone through more gene duplications that less highly evolved organisms, so they should have a larger genome size, but they do not. That is why Dr. Wile thinks that the C-value paradox refutes gene duplication as an important evolutionary mechanism.

However, evolution is a tree and not a ladder. All currently existing organisms, whether we label then as “simple” or “complex” are at the tips of the branches of the tree. They are equally “highly evolved”. The organisms alive today that we consider “simple” have had exactly the same amount of time to diverge from a common ancestor as extant organisms we consider “complex”. That is why evolution does not predict that “complex” organisms should have a larger genome that “simple” organism. That is why it is a creationist straw man.

Let’s anticipate an objection: if both extant “simple” and extant “complex” organisms have had equal time to diverge from a common ancestor, then why do they not have the same genome size? That could of course be because there is no reason to suppose that gene duplication occurs with the same rate in every lineage. They are probably more common in plants, for instance.

Et tu!

In his original post, Mr. Karlsson claims that it was a “straw man” for certain creationist videos to say that evolution is nothing more than random mutation plus natural selection. In my reply, I simply pointed out that evolutionists make that claim as well. Mr. Karlsson didn’t like the fact that I demonstrated this, so he tries to make excuses for the evolutionists, much like he tried to make excuses for Mr. Nye. He claims that the evolutionists were making “introductory descriptions of the field of evolutionary biology, not complete descriptions of a multifaceted scientific literature.”

That is certainly the case. However, what do you think the creationist videos responding to Mr. Nye are? They are introductory descriptions of the problems with evolutionary biology, not complete descriptions of a multifaceted scientific literature. It seems that Mr. Karlsson excuses evolutionists for saying that evolution is random mutation plus natural selection in introductory materials, but he doesn’t tolerate it when creationists do exactly the same thing.

Even setting aside the fact that this is an obvious case of two wrongs make a right fallacy, the argument fails spectacularly: the creationists where not providing “introductory descriptions of the problems with evolutionary biology”, but rather their view of what evolution was. So my complaint was about their description of evolution, not their descriptions of creationist problems with evolution. Thus, my argument evades Dr. Wile’s objection.

Molecular phylogeny and incomplete lineage sorting

He then says that I am ignoring incomplete lineage sorting. Of course I am, because it is an ad hoc hypothesis that is meant to explain away inconvenient data. Remember, his original claim is that comparing DNA sequences provides evidence for evolution. However, the data say otherwise. To explain around this inconvenient fact, incomplete lineage sorting was invented.

No, incomplete lineage sorting is used to explain the discrepancy between whole genome (or whole protein-coding genome) molecular phylogeny on the one hand and some molecular phylogeny of certain single genes. Why is that the case? The explanation is that single genes can be affected by genetic drift independent of other genes and so molecular phylogenies of the entire genome or that of the whole protein-coding parts of the genome is a statistical average for the relationship between all of the genes of two species. Since it is an averages, that means that the relatedness of individual genes in two organisms may be higher or lower than the average. Hardly a new and radical idea.

As an oversimplified analogy, consider the height between three different groups. One of the groups (A) have gotten good nutrition as children, the second (B) has gotten intermediate nutrition and the third (C) has gotten poor nutrition. So the averages are A > B > C. But this does not mean that every single individual in group B is taller than every single individual in C. It is entirely conceivable that the tallest person in group C is taller than the shortest person in group B. It could even be the case that the tallest C person is closer in height to individual in A than to a person in group B. Does this discovery refute the fact that that the average of B is not higher than the average of C? Of course not. Similarly, the average evolutionary relatedness between organism A and B may be higher than between A and C, yet C can have some particular alleles more evolutionarily related to the corresponding alleles in A.

Am I ignorant about what creationists believe?

Dr. Wile makes the following argument:

Creationists certainly do not believe that God created all the creatures we see today in their present form. Instead, creationists give strong evidence that God created archetypal creatures that then adapted into the huge variety we see today. For example, God created only one kind of doglike creature. After the Flood, however, the two doglike creatures that were preserved on the ark produced progeny that migrated and adapted to their new environments, producing wolves, coyotes, and domesticated dogs.

But I did not say that creationists believe that the creator made all the different creatures that we see today in their present form. What I said was that creationists believe that the creator made all the different creatures that we see today pretty much in their present form. As Dr. Wile explains it, creationists agree that there can be variation within each biblical kinds, but one kind cannot evolve to another or two different kinds cannot be evolutionarily related. So, contrary to what Dr. Wile claims, I am fully aware of this. Yet, as an added bonus, I will explain his argument about dog-like creatures fail.

Most young-earth creationists set the date of the Flood to somewhere around 4000 years ago (perhaps a bit earlier). For the purpose of this argument, the precise year does not matter. So Noah brings two dog-like creatures onto the Ark around 4000 years ago and after the water had subsided, these diversified to different versions of the “dog kind” such as wolves, coyotes, and dogs as we know them. There are two problems here: (1) rate of evolution and (2) inbreeding depression.

The domestication of the current lineage of dogs from wolves occurred around 15000 years ago (Larson et. al. 2012) according to the mainstream scientific position (incidentally, before the origin of the universe according to young-earth creationists). So to arrive at the current situation from just 4000 years ago, Dr. Wile has to postulate a rate of evolution that is many times higher than what we observe. In fact, since Dr. Wile believes that the two dog-like creatures stepping off the Ark was the ancestors of not only domesticated dogs, but of wolves and coyotes as well, the rate has to be postulated to be even higher. According to mainstream science, the coyote originated around 1.8 million years ago (click “age range and collections”). This means that Dr. Wile has to squeeze in almost 2 million years of evolution into just 4000 years. Ironically and contradictory, Dr. Wile simultaneously deny much of mainstream evolution, yet has to postulate an mutation rate and evolutionary rate during the past 4000 years that is several orders of magnitude higher than anything that has ever been observed in nature.

The second problem is inbreeding depression. If the population of dog-like creatures was just two at around 4000 years ago, the accumulation of recessive and harmful mutations would be enough to make the lineage go extinct. But clearly dogs, wolves and coyotes exist, making the literal Ark scenario implausible. The most common retort is to say that the genomes of the original dog-like creatures were without recessive mutations, but that does not matter as they would originate and accumulate during the 4000 years of incest. Maybe you can get away from inbreeding depression by actually agreeing that the mutation rate was astronomically high to be able to squeeze in ~2 million years worth of evolution into 4000 years, but they you are faced with another problem: such a high mutation rate would lead to genomic instability, cancer and death. However, I doubt that Dr. Wile wants to propose such a high mutation rate, which leaves him with both problems I discussed: he has to explain how the dog-like creature could diversify into wolves, dogs and coyote in such a short period of time and why inbreeding depression did not make the lineage go extinct. As far as I can tell, these problems are insurmountable.

Supernaturalism and the uniformity of nature

They showed that without the proper concept of a deity, science would never have developed. This, of course, is a well-established view among historians of science. The fact that Mr. Karlsson doesn’t know this demonstrates that he has not really investigated the issue of how science developed.

So Dr. Wile does not actually reply to my point: if you believe in a powerful and ultimately unpredictable supernatural entity, how could you ever know that the uniformity of nature is valid? Surely, this designer could have a morally justifiable reason to violate the uniformity of nature if he so wants? This means that on theism, science is impossible.

The claim that science would never have developed without “the proper concept of a deity” is of course wrong. Ancient Greece and China made great scientific advances, even without the belief in the deity of the bible. Furthermore, if Christian theism was so conducive to science, why did it take around 1000 years between the rise of Christianity in Rome to the scientific revolution? As ancient historian Richard Carrier (2010) puts it:

As the story now goes, not only has Christianity never been at odds with science and never impeded it in any way, but it was actu­ally the savior of science, the only worldview that could ever make science possible. And that’s why the Scientific Revolution only ever sparked in one place: a thoroughly Christian society.

This is not only false in every conceivable detail but so egregiously false that anyone with even the slightest academic competence and respon­sibility should have known it was false. Which means its advocates, all of whom claim to be scholars, must either be embarrassingly incompetent, perversely dishonest, or wildly deluded.

[…]

An obvious objection to this delusional claim is that it violates one of the most basic principles of causality: when the cause is in place, its effect is seen. Christianity fully dominated the whole of the Western world from the fifth to the fifteenth century, and yet in all those thousand years there was no Scientific Revolution. A cause that fails to have its predicted effect despite being continually in action for a thousand years is usually consid­ered refuted, not confirmed.

Saying that because modern science arose in a Christian culture, this means that that science would never have developed without Christian theism is just as absurd as saying that axiomatic geometry requires polytheism because it happened to arise in a polytheistic culture. Correlation does not imply causation.

As you can see, then, Mr. Karlsson’s reply to me has more errors than his initial post. Of course, that’s to be expected. Anyone who is anti-science enough to defend Mr. Nye’s video is not going to present science or its origins in any serious way.

Pot, meet kettle.

References and further reading

Flajnik, M. F., & Kasahara, M. (2010). Origin and evolution of the adaptive immune system: genetic events and selective pressures. Nat Rev Genet, 11(1), 47-59.

Larson, G., Karlsson, E. K., Perri, A., Webster, M. T., Ho, S. Y. W., Peters, J., . . . Lindblad-Toh, K. (2012). Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proceedings of the National Academy of Sciences, 109(23), 8878-8883. doi: 10.1073/pnas.1203005109